New methods have been developed to choose probable protein secondary conformations. Direct interatomic interaction energies are calculated to yield probabilities of various conformers. Approximate energies of all possible alpha-helix and beta-strand segments are calculated. Electrostatic energies are calculated in detail, in the approximation of mean side chain positions. The remainder of the energy is approximated with a contribution from each residue in alpha-helix. Glycine residues are taken to have a different value of this parameter than other residues. Two methods for selecting a best set of molecular conformations are compared: 1) energy minimization, in which the molecular energy is taken as the sum of the energies of independent secondary regions and 2) conformational probabilities for each residue calculated from the eneriges of all possible combinations of secondary regions. The two methods yield approximately the same secondary conformations which, for energy minimization, are correct for 65% of all residues and for 83% of all residues in regular secondary regions, averaged over six proteins.